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- PDB-5szb: Structure of human Dpf3 double-PHD domain bound to histone H3 tai... -

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Basic information

Entry
Database: PDB / ID: 5szb
TitleStructure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14
Components
  • Histone H3 tail peptide
  • Zinc finger protein DPF3
KeywordsPEPTIDE BINDING PROTEIN / chromatin / modified histone / PHD domain / zinc binding domain / BAF45 / BAF complex / PEPTIDE-BINDING PROTEIN
Function / homology
Function and homology information


nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of myoblast differentiation ...nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of myoblast differentiation / regulation of G1/S transition of mitotic cell cycle / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / positive regulation of cell differentiation / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / nervous system development / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex / DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / membrane / nucleus
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Zinc finger protein DPF3 / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsSingh, N. / Local, A. / Shiau, A. / Ren, B. / Corbett, K.D.
CitationJournal: Nat. Genet. / Year: 2018
Title: Identification of H3K4me1-associated proteins at mammalian enhancers.
Authors: Local, A. / Huang, H. / Albuquerque, C.P. / Singh, N. / Lee, A.Y. / Wang, W. / Wang, C. / Hsia, J.E. / Shiau, A.K. / Ge, K. / Corbett, K.D. / Wang, D. / Zhou, H. / Ren, B.
History
DepositionAug 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_keywords.text
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein DPF3
H: Histone H3 tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2527
Polymers14,8722
Non-polymers3805
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area7340 Å2
MethodPISA
2
A: Zinc finger protein DPF3
H: Histone H3 tail peptide
hetero molecules

A: Zinc finger protein DPF3
H: Histone H3 tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,50414
Polymers29,7444
Non-polymers76010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
Buried area5300 Å2
ΔGint-31 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.321, 39.321, 147.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-648-

HOH

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Components

#1: Protein Zinc finger protein DPF3 / BRG1-associated factor 45C / BAF45C / Zinc finger protein cer-d4


Mass: 12881.659 Da / Num. of mol.: 1 / Fragment: double-PHD domain (UNP residues 254-368)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92784
#2: Protein/peptide Histone H3 tail peptide


Mass: 1990.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: V9H1G0, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2016 / Details: Mirror: Rh coated flat, toroidal focusing
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→39.61 Å / Num. obs: 38299 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 8.2 / CC1/2: 0.978 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→37.996 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 11.98
RfactorNum. reflection% reflection
Rfree0.1554 5820 8.26 %
Rwork0.138 --
obs0.1394 70420 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→37.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 12 177 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011053
X-RAY DIFFRACTIONf_angle_d1.391432
X-RAY DIFFRACTIONf_dihedral_angle_d13.291397
X-RAY DIFFRACTIONf_chiral_restr0.094154
X-RAY DIFFRACTIONf_plane_restr0.007186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1911-1.20470.1622110.13232019X-RAY DIFFRACTION96
1.2047-1.21880.27181870.22632139X-RAY DIFFRACTION99
1.2188-1.23370.18471720.15022184X-RAY DIFFRACTION99
1.2337-1.24930.132190.11172099X-RAY DIFFRACTION100
1.2493-1.26580.14011890.11772201X-RAY DIFFRACTION100
1.2658-1.28310.161770.14082108X-RAY DIFFRACTION98
1.2831-1.30140.2632120.21572129X-RAY DIFFRACTION98
1.3014-1.32090.14262030.12042148X-RAY DIFFRACTION100
1.3209-1.34150.15252010.11852115X-RAY DIFFRACTION100
1.3415-1.36350.15321900.11832222X-RAY DIFFRACTION100
1.3635-1.3870.14831970.11162111X-RAY DIFFRACTION100
1.387-1.41220.14761980.11152182X-RAY DIFFRACTION100
1.4122-1.43940.1481940.11012139X-RAY DIFFRACTION100
1.4394-1.46880.13441980.10882176X-RAY DIFFRACTION100
1.4688-1.50070.11941950.10372165X-RAY DIFFRACTION100
1.5007-1.53560.15011930.10252167X-RAY DIFFRACTION100
1.5356-1.5740.12041950.10282205X-RAY DIFFRACTION100
1.574-1.61660.13871910.09822113X-RAY DIFFRACTION100
1.6166-1.66420.11211970.09962157X-RAY DIFFRACTION100
1.6642-1.71790.14571830.09772177X-RAY DIFFRACTION100
1.7179-1.77930.10741990.10842177X-RAY DIFFRACTION100
1.7793-1.85050.11661940.1142151X-RAY DIFFRACTION100
1.8505-1.93470.16131810.15042128X-RAY DIFFRACTION100
1.9347-2.03670.11931960.12542185X-RAY DIFFRACTION100
2.0367-2.16430.14081860.12672168X-RAY DIFFRACTION100
2.1643-2.33140.15891870.15522179X-RAY DIFFRACTION100
2.3314-2.5660.15661970.14732147X-RAY DIFFRACTION100
2.566-2.93720.19151880.15692181X-RAY DIFFRACTION100
2.9372-3.70.17121950.15742169X-RAY DIFFRACTION100
3.7-38.01510.18141950.17032159X-RAY DIFFRACTION100

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